Genetic Variant LRRC61:c.-145+3654T>C (chr7-150329664-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001142928.2(LRRC61):c.-145+3654T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,252 control chromosomes in the GnomAD database, including 3,828 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.22 ( 3827 hom., cov: 33)

Exomes 𝑓: 0.31 ( 1 hom. )

Consequence

LRRC61
NM_001142928.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.381

Publications

21 publications found

Variant links:

Genes affected

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LRRC61 links:

ENSG00000293476 (HGNC:):

ENSG00000293476 links:

ZBED10P (HGNC:21720): (zinc finger BED-type containing 10, pseudogene)

ZBED10P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
LRRC61	NM_001142928.2 link	c.-145+3654T>C	intron_variant	Intron 2 of 2	ENST00000359623.9	NP_001136400.1	Q9BV99A0A090N7W5
LRRC61	NM_001363433.1 link	c.-145+3654T>C	intron_variant	Intron 2 of 2		NP_001350362.1
LRRC61	NM_001363434.1 link	c.-145+3654T>C	intron_variant	Intron 2 of 2		NP_001350363.1
LRRC61	NM_023942.3 link	c.-145+6104T>C	intron_variant	Intron 1 of 1		NP_076431.1	Q9BV99A0A090N7W5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC61	ENST00000359623.9 link	c.-145+3654T>C		intron_variant	Intron 2 of 2	2	NM_001142928.2	ENSP00000352642.4		Q9BV99

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32969

AN:

152108

Hom.:

3836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.201

GnomAD4 exome

AF:

0.308

AC:

AN:

Hom.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.567

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.217

AC:

32975

AN:

152226

Hom.:

3827

Cov.:

AF XY:

0.218

AC XY:

16192

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.152

AC:

6298

AN:

41524

American (AMR)

AF:

0.148

AC:

2265

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

1076

AN:

3470

East Asian (EAS)

AF:

0.290

AC:

1504

AN:

5178

South Asian (SAS)

AF:

0.270

AC:

1305

AN:

4828

European-Finnish (FIN)

AF:

0.247

AC:

2615

AN:

10598

Middle Eastern (MID)

AF:

0.236

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.251

AC:

17069

AN:

68014

Other (OTH)

AF:

0.198

AC:

419

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1326

2652

3979

5305

6631

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.230

Hom.:

1487

Bravo

AF:

0.204

Asia WGS

AF:

0.270

AC:

942

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.0

(source)

DANN

Benign

0.77

PhyloP100

0.38

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over